Sign upLogin

KarrLab/obj_tables

View on GitHub
Star
obj_tables/__main__.py

Summary

Maintainability
D
2 days
Test Coverage
A
95%

File __main__.py has 307 lines of code (exceeds 250 allowed). Consider refactoring.
Open

""" Command line utilities for modeling data in tables (XLSX, CSV, TSV)

:Author: Jonathan Karr <karr@mssm.edu>
:Date: 2019-09-11
:Copyright: 2019, Karr Lab
Severity: Minor
Found in obj_tables/__main__.py - About 3 hrs to fix

    Function main has a Cognitive Complexity of 9 (exceeds 5 allowed). Consider refactoring.
    Open

    def main():
    with App() as app:
        try:
            app.run()
        except SystemExit as exception:
    Severity: Minor
    Found in obj_tables/__main__.py - About 55 mins to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Function _default has a Cognitive Complexity of 7 (exceeds 5 allowed). Consider refactoring.
    Open

        def _default(self):
        args = self.app.pargs
        schema_name, schema, models = get_schema_models(args.schema_file)
        for model in models:
            if model.__name__ == args.model:
    Severity: Minor
    Found in obj_tables/__main__.py - About 35 mins to fix

    Cognitive Complexity

    Cognitive Complexity is a measure of how difficult a unit of code is to intuitively understand. Unlike Cyclomatic Complexity, which determines how difficult your code will be to test, Cognitive Complexity tells you how difficult your code will be to read and comprehend.

    A method's cognitive complexity is based on a few simple rules:

    • Code is not considered more complex when it uses shorthand that the language provides for collapsing multiple statements into one
    • Code is considered more complex for each "break in the linear flow of the code"
    • Code is considered more complex when "flow breaking structures are nested"

    Further reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'init-schema'
        description = 'Initialize a Python schema from a declarative description of the schema in a table (XLSX, CSV, TSV)'
        help = 'Initialize a Python schema from a declarative description of the schema in a table (XLSX, CSV, TSV)'
        stacked_on = 'base'
    Severity: Major
    Found in obj_tables/__main__.py and 2 other locations - About 3 hrs to fix
    obj_tables/__main__.py on lines 239..248
    obj_tables/__main__.py on lines 269..278

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 63.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'validate'
        description = 'Validate that a workbook is consistent with a schema, and report any errors'
        help = 'Validate that a workbook is consistent with a schema, and report any errors'
        stacked_on = 'base'
    Severity: Major
    Found in obj_tables/__main__.py and 2 other locations - About 3 hrs to fix
    obj_tables/__main__.py on lines 128..137
    obj_tables/__main__.py on lines 269..278

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 63.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Similar blocks of code found in 3 locations. Consider refactoring.
    Open

        class Meta:
        label = 'viz-schema'
        description = 'Generate a UML diagram for a schema'
        help = 'Generate a UML diagram for a schema'
        stacked_on = 'base'
    Severity: Major
    Found in obj_tables/__main__.py and 2 other locations - About 3 hrs to fix
    obj_tables/__main__.py on lines 128..137
    obj_tables/__main__.py on lines 239..248

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 63.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

            io.Writer().run(args.out_wb_file, objs,
                        schema_name=schema_name,
                        doc_metadata=reader._doc_metadata,
                        model_metadata=reader._model_metadata,
                        models=models, write_toc=args.write_toc, write_schema=args.write_schema,
    Severity: Major
    Found in obj_tables/__main__.py and 1 other location - About 2 hrs to fix
    obj_tables/__main__.py on lines 227..232

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 54.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    Identical blocks of code found in 2 locations. Consider refactoring.
    Open

            io.Writer().run(args.out_wb_file, objs,
                        schema_name=schema_name,
                        doc_metadata=reader._doc_metadata,
                        model_metadata=reader._model_metadata,
                        models=models, write_toc=args.write_toc, write_schema=args.write_schema,
    Severity: Major
    Found in obj_tables/__main__.py and 1 other location - About 2 hrs to fix
    obj_tables/__main__.py on lines 83..88

    Duplicated Code

    Duplicated code can lead to software that is hard to understand and difficult to change. The Don't Repeat Yourself (DRY) principle states:

    Every piece of knowledge must have a single, unambiguous, authoritative representation within a system.

    When you violate DRY, bugs and maintenance problems are sure to follow. Duplicated code has a tendency to both continue to replicate and also to diverge (leaving bugs as two similar implementations differ in subtle ways).

    Tuning

    This issue has a mass of 54.

    We set useful threshold defaults for the languages we support but you may want to adjust these settings based on your project guidelines.

    The threshold configuration represents the minimum mass a code block must have to be analyzed for duplication. The lower the threshold, the more fine-grained the comparison.

    If the engine is too easily reporting duplication, try raising the threshold. If you suspect that the engine isn't catching enough duplication, try lowering the threshold. The best setting tends to differ from language to language.

    See codeclimate-duplication's documentation for more information about tuning the mass threshold in your .codeclimate.yml.

    Refactorings

    Further Reading

    There are no issues that match your filters.

    Category
    Status